Does DBOOT do the actual similarity/distance calculations or does it just produced bootstrapped sets of data? Looking at a couple of papers that use DBOOT (
Lima et al., 2002; Bruel et al., 2006
(PDF)), they both seem to use the Jaccard-similarity coefficient (JSC), although they each calculate it slightly differently, but it isn't clear if that is the metric that DBOOT itself uses.
So for the JSC for these two samples:
Sample
i:111100001010010000111100001
Sample
j:100111001000100100010010000
JSC
ij = a/(a+b+c) = 4/(4+8+5) =0.235
Where a is the number of polymorphic bands present in both individuals, b is the number of bands present in
i and absent in
j, and c is the number of bands present in
j and absent in
i. Bands absent in both individuals are ignored.
The distance would be the complement of the JSC: 1 - 0.235 = 0.765
The difference between this method and the simple matching based one you use is that it does not count matching 0 values towards similarity. Using your method I believe the distance measure would be ~0.481, considerably more similar.
Perhaps using the JSC would give you results more in line with the DBOOT program.
TTFN,
WK
Edited by Wounded King, : No reason given.
™ Version 4.2
